I don't have extensive experience with PXIe systems, but have made some systems in the past and present. A current system collects data continuously at 20-30MSa/s for 32 channels. At that rate the 15TB RAID array is filled up in a few hours.
Advantages:
Throughput. Unless your modular instruments are attached via thunderbolt, hard to beat PXIe throughput. However, it might not be needed in your case.
Triggering. Simple to implement triggering or advanced triggering through the backplane. Can be done with modular instruments also, but more wires and more hassles. If you need a synchronized start, the PXI backplane is your friend.
Synchronization. Can share reference/sample clocks through the backplane. Can be done with modular instruments also, but more wires and more hassles.
Compact. Somewhat more compact than modular instruments.
Disadvantages.
Expensive. Noted in previous message.
Support. If you have instruments from different vendors and there is a problem, each vendor may blame the other. I had a chassis, a controller, and digitizers from three different companies. When there was an issue with the cards and the slots they could occupy, everyone at first blamed the other, Eventually, it was found that the chassis had an issue with the interrupts. PXI is supposed to be standardized but ...
Future proof. The embedded PXIe controllers seem to always be a generation or two behind current CPU offerings. In addition, their components are difficult to upgrade or have limited upgrade capabilities. You may want to also purchase an external TB controller card. This allows to you to attach the chassis to a computer via the TB port and control from that computer instead of using an embedded controller.